How to sequence and annotate insect mitochondrial genomes for systematic and comparative genomics research

Cameron, Stephen L. (2014) How to sequence and annotate insect mitochondrial genomes for systematic and comparative genomics research. Systematic Entomology, 39(3), pp. 400-411.

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Abstract

Over the past decade the mitochondrial (mt) genome has become the most widely used genomic resource available for systematic entomology. While the availability of other types of ‘–omics’ data – in particular transcriptomes – is increasing rapidly, mt genomes are still vastly cheaper to sequence and are far less demanding of high quality templates. Furthermore, almost all other ‘–omics’ approaches also sequence the mt genome, and so it can form a bridge between legacy and contemporary datasets. Mitochondrial genomes have now been sequenced for all insect orders, and in many instances representatives of each major lineage within orders (suborders, series or superfamilies depending on the group). They have also been applied to systematic questions at all taxonomic scales from resolving interordinal relationships (e.g. Cameron et al., 2009; Wan et al., 2012; Wang et al., 2012), through many intraordinal (e.g. Dowton et al., 2009; Timmermans et al., 2010; Zhao et al. 2013a) and family-level studies (e.g. Nelson et al., 2012; Zhao et al., 2013b) to population/biogeographic studies (e.g. Ma et al., 2012). Methodological issues around the use of mt genomes in insect phylogenetic analyses and the empirical results found to date have recently been reviewed by Cameron (2014), yet the technical aspects of sequencing and annotating mt genomes were not covered. Most papers which generate new mt genome report their methods in a simplified form which can be difficult to replicate without specific knowledge of the field. Published studies utilize a sufficiently wide range of approaches, usually without justification for the one chosen, that confusion about commonly used jargon such as ‘long PCR’ and ‘primer walking’ could be a serious barrier to entry. Furthermore, sequenced mt genomes have been annotated (gene locations defined) to wildly varying standards and improving data quality through consistent annotation procedures will benefit all downstream users of these datasets.

The aims of this review are therefore to:

  1. Describe in detail the various sequencing methods used on insect mt genomes;

  2. Explore the strengths/weakness of different approaches;

  3. Outline the procedures and software used for insect mt genome annotation, and;

  4. Highlight quality control steps used for new annotations, and to improve the re-annotation of previously sequenced mt genomes used in systematic or comparative research.

Impact and interest:

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33 citations in Web of Science®

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ID Code: 73195
Item Type: Journal Article
Refereed: Yes
Keywords: Mitochondrial (mt) Genome, Systematic Entomology, Sequencing, Insects
DOI: 10.1111/syen.12071
ISSN: 0307-6970
Divisions: Current > Schools > School of Earth, Environmental & Biological Sciences
Current > QUT Faculties and Divisions > Science & Engineering Faculty
Copyright Owner: Copyright 2014 The Royal Entomological Society
Deposited On: 03 Jul 2014 00:29
Last Modified: 04 Aug 2015 15:21

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